add patch for chromosomes not found in gtf

colomemaria / epiScanpy

Episcanpy: Epigenomics Single Cell Analysis in Python

BSD 3-Clause "New" or "Revised" License

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add patch for chromosomes not found in gtf #105

Closed mvinyard closed 3 years ago

mvinyard commented 3 years ago

Some chromosomes in AnnData are not found in the gtf. In this case, nothing is appended to gene_index and this prevents gene_annotations from being merged into adata.var DataFrame.

I tested this with outputs from CellRanger 2.0 and the matching genes.gtf file.

mvinyard commented 3 years ago

Seems like this was fixed in another/concurrent PR. closing.